Next generation diagnostics of cystic fibrosis and CFTR-related disorders by targeted multiplex high-coverage resequencing of CFTR

Journal of Medical Genetics

Volumn 50, Issue 7, 2013, Pages 455-462

  Trujillano, D ^a,b,c,d   Ramos, M D ^e   Gonzalez J ^a,b,c,d   Tornador, C ^a,b,c,d   Sotillo, F ^e   Escaramis, G ^a,b,c,d   Ossowski, S ^a,b   Armengol, L ^f   Casals, T ^e   Estivill, X ^a,b,c,d  

^a CENTRE FOR GENOMIC REGULATION CRG   (Spain)

^b UNIVERSITAT POMPEU FABRA   (Spain)

^c HOSPITAL DEL MAR   (Spain)

^d CIBER EPIDEMIOLOGÍA Y SALUD PÚBLICA CIBERESP   (Spain)

^e BELLVITGE BIOMEDICAL RESEARCH INSTITUTE IDIBELL   (Spain)

^f QGenomics Laboratory   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

CYSTIC FIBROSIS TRANSMEMBRANE CONDUCTANCE REGULATOR;

ADULT; ARTICLE; BIOINFORMATICS; CYSTIC FIBROSIS; DNA LIBRARY; EXON; FEMALE; GENE DELETION; GENE MUTATION; GENE REARRANGEMENT; GENETIC ALGORITHM; GENETIC POLYMORPHISM; GENETIC VARIABILITY; HAPLOTYPE; HUMAN; INDEL MUTATION; MAJOR CLINICAL STUDY; NONHUMAN; POINT MUTATION; PRIORITY JOURNAL;

EID: 84883194528     PISSN: 00222593     EISSN: 14686244     Source Type: Journal    
DOI: 10.1136/jmedgenet-2013-101602     Document Type: Article

References (29)

1. Farrell PM. The prevalence of cystic fibrosis in the European Union. J Cyst Fibros 2008;7:450-3.
2. O'Sullivan BP, Freedman SD. Cystic fibrosis. Lancet 2009;373:1891-904.
3. Bobadilla JL, Macek M Jr, Fine JP, Farrell PM. Cystic fibrosis: a worldwide analysis of CFTR mutations-correlation with incidence data and application to screening. Hum Mutat 2002;19:575-606.
4. Estivill X, Bancells C, Ramos C. Geographic distribution and regional origin of 272 cystic fibrosis mutations in European populations. The Biomed CF Mutation Analysis Consortium. Hum Mutat 1997;10:135-54.
5. Kerem B, Rommens JM, Buchanan JA, Markiewicz D, Cox TK, Chakravarti A, Buchwald M, Tsui LC. Identification of the cystic fibrosis gene: genetic analysis. Science 1989;245:1073-80.
6. Riordan JR, Rommens JM, Kerem B, Alon N, Rozmahel R, Grzelczak Z, Zielenski J, Lok S, Plavsic N, Chou JL, Drumm ML, Iannuzzi MC, Collins FS, Tsui LC. Identification of the cystic fibrosis gene: cloning and characterization of complementary DNA. Science 1989;245:1066-73.
7. Rommens JM, Iannuzzi MC, Kerem B, Drumm ML, Melmer G, Dean M, Rozmahel R, Cole JL, Kennedy D, Hidaka N, Zsiga M, Buchwald M, Riordan JR, Tsui LC, Collin FS. Identification of the cystic fibrosis gene: chromosome walking and jumping. Science 1989;245:1059-65.
8. Dequeker E, Stuhrmann M, Morris MA, Casals T, Castellani C, Claustres M, Cuppens H, des Georges M, Ferec C, Macek M, Pignatti PF, Scheffer H, Schwartz M, Witt M, Schwarz M, Girodon E. Best practice guidelines for molecular genetic diagnosis of cystic fibrosis and CFTR-related disorders-updated European recommendations. Eur J Hum Genet 2009;17:51-65.
9. Chillon M, Casals T, Mercier B, Bassas L, Lissens W, Silber S, Romey MC, Ruiz-Romero J, Verlingue C, Claustres M, Nunes V, Férec C, Estivill X. Mutations in the cystic fibrosis gene in patients with congenital absence of the vas deferens. N Engl J Med 1995;332:1475-80.
10. Ramos MD, Masvidal L, Gimenez J, Bieth E, Seia M, des Georges M, Armengol L, Casals T. CFTR rearrangements in Spanish cystic fibrosis patients: first new duplication (35kb) characterised in the Mediterranean countries. Ann Hum Genet 2010;74:463-9.
11. Alonso MJ, Heine-Suner D, Calvo M, Rosell J, Gimenez J, Ramos MD, Telleria JJ, Palacio A, Estivill X, Casals T. Spectrum of mutations in the CFTR gene in cystic fibrosis patients of Spanish ancestry. Ann Hum Genet 2007;71(Pt 2):194-201.
12. Walsh T, Lee MK, Casadei S, Thornton AM, Stray SM, Pennil C, Nord AS, Mandell JB, Swisher EM, King MC. Detection of inherited mutations for breast and ovarian cancer using genomic capture and massively parallel sequencing. Proc Natl Acad Sci USA 2010;107:12629-33.
13. Kumar P, Henikoff S, Ng PC. Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat Protoc 2009;4:1073-81.
14. Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, Kondrashov AS, Sunyaev SR. A method and server for predicting damaging missense mutations. Nat Methods 2010;7:248-9.
15. Cooper GM, Stone EA, Asimenos G, Green ED, Batzoglou S, Sidow A. Distribution and intensity of constraint in mammalian genomic sequence. Genome Res 2005;15:901-13.
16. Schwarz JM, Rodelsperger C, Schuelke M, Seelow D. MutationTaster evaluates disease-causing potential of sequence alterations. Nat Methods 2010;7:575-6.
17. Groman JD, Hefferon TW, Casals T, Bassas L, Estivill X, Des Georges M, Guittard C, Koudova M, Fallin MD, Nemeth K, Fekete G, Kadasi L, Friedman K, Schwarz M, Bombieri C, Pignatti PF, Kanavakis E, Tzetis M, Schwartz M, Novelli G, D'Apice MR, Sobczynska-Tomaszewska A, Bal J, Stuhrmann M, Macek M Jr, Claustres M, Cutting GR. Variation in a repeat sequence determines whether a common variant of the cystic fibrosis transmembrane conductance regulator gene is pathogenic or benign. Am J Hum Genet 2004;74:176-9.
18. Ferec C, Casals T, Chuzhanova N, Macek M Jr, Bienvenu T, Holubova A, King C, McDevitt T, Castellani C, Farrell PM, Sheridan M, Pantaleo SJ, Loumi O, Messaoud T, Cuppens H, Torricelli F, Cutting GR, Williamson R, Ramos MJ, Pignatti PF, Raguenes O, Cooper DN, Audrezet MP, Chen JM. Gross genomic rearrangements involving deletions in the CFTR gene: characterization of six new events from a large cohort of hitherto unidentified cystic fibrosis chromosomes and meta-analysis of the underlying mechanisms. Eur J Hum Genet 2006;14:567-76.
19. Dork T, Macek M Jr, Mekus F, Tummler B, Tzountzouris J, Casals T, Krebsova A, Koudova M, Sakmaryova I, Macek M Sr, Vavrova V, Zemkova D, Ginter E, Petrova NV, Ivaschenko T, Baranov V, Witt M, Pogorzelski A, Bal J, Zekanowsky C, Wagner K, Stuhrmann M, Bauer I, Seydewitz HH, Neumann T, Jakubiczka S. Characterization of a novel 21-kb deletion, CFTRdele2,3(21 kb), in the CFTR gene: a cystic fibrosis mutation of Slavic origin common in Central and East Europe. Hum Genet 2000;106:259-68.
20. Chevalier-Porst F, Souche G, Bozon D. Identification and characterization of three large deletions and a deletion/polymorphism in the CFTR gene. Hum Mutat 2005;25:504.
21. Morral N, Nunes V, Casals T, Cobos N, Asensio O, Dapena J, Estivill X. Uniparental inheritance of microsatellite alleles of the cystic fibrosis gene (CFTR): identification of a 50 kilobase deletion. Hum Mol Genet 1993;2:677-81.
22. Lerer I, Laufer-Cahana A, Rivlin JR, Augarten A, Abeliovich D. A large deletion mutation in the CFTR gene (3120+1Kbdel8.6Kb): a founder mutation in the Palestinian Arabs. Mutation in brief no. 231. Online. Hum Mutat 1999;13:337.
23. Casals T, Bassas L, Egozcue S, Ramos MD, Gimenez J, Segura A, Garcia F, Carrera M, Larriba S, Sarquella J, Estivill X. Heterogeneity for mutations in the CFTR gene and clinical correlations in patients with congenital absence of the vas deferens. Hum Reprod 2000;15:1476-83.
24. Casals T, De-Gracia J, Gallego M, Dorca J, Rodriguez-Sanchon B, Ramos MD, Gimenez J, Cistero-Bahima A, Olveira C, Estivill X. Bronchiectasis in adult patients: an expression of heterozygosity for CFTR gene mutations?. Clin Genet 2004;65:490-5.
25. Casals T, Aparisi L, Martinez-Costa C, Gimenez J, Ramos MD, Mora J, Diaz J, Boadas J, Estivill X, Farre A. Different CFTR mutational spectrum in alcoholic and idiopathic chronic pancreatitis?. Pancreas 2004;28:374-9.
26. Redin C, Le Gras S, Mhamdi O, Geoffroy V, Stoetzel C, Vincent MC, Chiurazzi P, Lacombe D, Ouertani I, Petit F, Till M, Verloes A, Jost B, Chaabouni HB, Dollfus H, Mandel JL, Muller J. Targeted high-throughput sequencing for diagnosis of genetically heterogeneous diseases: efficient mutation detection in Bardet-Biedl and Alstrom Syndromes. J Med Genet 2012;49:502-12.
27. Wetterstrand KA. DNA Sequencing Costs: Data from the NHGRI Large-Scale Genome Sequencing Program. http://www.genome.gov/sequencingcosts (accessed Nov 2012).
28. Saunders CJ, Miller NA, Soden SE, Dinwiddie DL, Noll A, Alnadi NA, Andraws N, Patterson ML, Krivohlavek LA, Fellis J, Humphray S, Saffrey P, Kingsbury Z, Weir JC, Betley J, Grocock RJ, Margulies EH, Farrow EG, Artman M, Safina NP, Petrikin JE, Hall KP, Kingsmore SF. Rapid whole-genome sequencing for genetic disease diagnosis in neonatal intensive care units. Sci Transl Med 2012;4:154ra35.
29. Krumm N, Sudmant PH, Ko A, O'Roak BJ, Malig M, Coe BP, Quinlan AR, Nickerson DA, Eichler EE. Copy number variation detection and genotyping from exome sequence data. Genome Res 2012;22:1525-32